Notes on DNA Structure and Replication from Lectures 15-21

Instructor Information

  • Name: Ben Lin, PhD

  • Position: Assistant Professor in the Department of Biochemistry and Cell Biology

  • Email: Benjamin.c.lin@stonybrook.edu

  • Office Location: Life Sciences Building 340

  • Office Hours: 11:00 AM – 12:00 PM on Mondays/Wednesdays, also by appointment via email

Course Overview

  • Lectures Covered: 7 Lectures (Chapters 12-16 from Campbell BIOLOGY, 12th edition)

  • First Lecture Focus: Chapter 16 on DNA replication before discussing the cell cycle

  • Assessments: 5 Chapter quizzes and 1 exam (online on 4/16/25 during class time)

  • Point Solutions Clicker Questions: Used throughout lectures to gauge comprehension (not graded)

  • Studying Resources: Readings from textbooks, animations, and HHMI BioInteractive resources available on Brightspace

Learning Objectives for Lecture 15: The Molecular Basis of Inheritance

  • Understand key historical experiments that identified DNA as genetic material:

    • Frederick Griffith’s bacterial transformation

    • Avery, MacLeod, and McCarty’s experiments

    • Hershey-Chase experiments using bacteriophages

  • Explain the structure of DNA and its components: nucleotides, base pairs

  • Detail DNA replication mechanisms including major proteins and roles

  • Differentiate leading and lagging strands during replication

  • Discuss telomeres: structure, function, and relation to cell proliferation

  • Describe chromatin composition and structure

Historical Context

  • Early 20th century findings:

    • Thomas Hunt Morgan’s chromosomal theory of inheritance established that genes are located on chromosomes, which are composed of DNA and proteins.

  • Key Question: Is DNA or protein the heritable genetic material?

Seminal Experiments

  1. Griffith’s Bacterial Transformation Experiment:

    • Studied pathogenic (S-Strain) vs. non-pathogenic (R-Strain) bacteria.

    • Found that heat-killed S bacteria could transform R bacteria into S bacteria, suggesting a transforming substance.

  2. Avery, McLeod, and McCarty's Experiment:

    • Confirmed that DNA is the transforming substance.

    • When nucleases destroyed DNA, transformation did not occur.

  3. Hershey-Chase Experiment:

    • Used T2 phages to test whether DNA or protein was the genetic material.

    • Found that only when phage DNA (labeled with radioactive phosphorus) was injected into bacteria did new phages form, confirming DNA as genetic material.

DNA Structure

  • Nucleotides:

    • Composed of a phosphate group, sugar, and nitrogenous base (A, T, C, G).

    • Pyrimidines: Thymine (T), Cytosine (C); Purines: Adenine (A), Guanine (G).

  • Phosphodiester Bonds: Connect nucleotides between the 3' OH and 5' phosphate group, creating directional strands (5' to 3').

Chargaff’s Rules

  • Base Composition Analysis:

    1. The amount of Adenine (A) equals Thymine (T); the amount of Cytosine (C) equals Guanine (G).

    2. The base composition varies between species, which explains biological diversity.

DNA Helical Structure

  • Proposed by Watson and Crick based on Rosalind Franklin's X-ray diffraction data, revealing a double helix structure.

  • Base pairing mechanism:

    • A pairs with T (two hydrogen bonds) and G pairs with C (three hydrogen bonds), consistent with Chargaff’s rules.

DNA Replication

  • Basic Concept: Semi-conservative model where each daughter DNA contains one old and one new strand.

  • Enzymes involved:

    • DNA Polymerase: Synthesizes DNA by adding nucleotides; works 5' to 3'.

    • Primase: Lays down RNA primer to provide a starting point for DNA synthesis.

    • Topoisomerase & Helicase: Unwind the DNA helix and relieve tension.

    • Single-strand binding proteins: Stabilize unwound strands during replication.

Leading vs. Lagging Strand Synthesis

  • Leading Strand: Synthesized continuously in the direction of the replication fork.

  • Lagging Strand: Synthesized discontinuously in segments called Okazaki fragments, which are later joined by DNA ligase.

Telomeres

  • Structure: Composed of repetitive sequences that protect chromosome ends.

  • Associated with aging; telomere shortening linked to cellular senescence.

  • Telomerase: Enzyme that extends telomeres in certain cells by adding telomeric repeats to the 3' ends of chromosomes.

Chromatin Structure

  • Euchromatin vs. Heterochromatin:

    • Euchromatin: Loosely packed, accessible for gene expression.

    • Heterochromatin: Densely packed, generally not accessible for transcription.

  • Basic unit of DNA packing is the nucleosome, where DNA wraps around histone proteins.